I was mousing over ship maintenance many times in the ship designer and ships. I did not see any reduction in my ship maintenance. Finally found the reason.

Below is the lines from the RaceTraitDefs.xml. The "<EffectType>ShipMaintenance</EffectType>" below should say "<EffectType>Maintenance</EffectType>" The ship maintenance reduction finally worked after changing "ShipMaintenance" to "Maintenance"

Four of the entries in the xml are bugged, Handy1, Handy2, Handy3, and Handy4.

Edit: RaceTraitsDefs.xml might not be bugged, other xmls might be the ones bugged?

<RaceTrait>
    <InternalName>Handy1</InternalName>
    <DisplayName>Handy1_Name</DisplayName>
    <Description>Handy1_Desc</Description>
    <Mod>
      <EffectType>ShipMaintenance</EffectType>
      <Scope>Global</Scope>
      <Target>
        <TargetType>Ship</TargetType>
      </Target>
      <BonusType>Multiplier</BonusType>
      <Value>-0.2</Value>
    </Mod>
    <Mod>
      <EffectType>Maintenance</EffectType>
      <Scope>Global</Scope>
      <Target>
        <TargetType>Colony</TargetType>
      </Target>
      <BonusType>Multiplier</BonusType>
      <Value>-0.2</Value>
    </Mod>
  </RaceTrait>

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Second example from GalCiv3AIDefs.xml, bonuses on Godlike difficulty.

I noticed there's no "ShipMaintenance"

<Stats>
    <EffectType>Maintenance</EffectType>
    <Scope>Global</Scope>
    <Target>
     <TargetType>Improvement</TargetType>
    </Target>
    <BonusType>Multiplier</BonusType>
    <Value>-0.5</Value>
   </Stats>   
   <Stats>
    <EffectType>Maintenance</EffectType>
    <Scope>Global</Scope>
    <Target>
     <TargetType>Ship</TargetType>
    </Target>
    <BonusType>Multiplier</BonusType>
    <Value>-0.5</Value>